9BC2 | pdb_00009bc2

Transglutaminase 2 - Open State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.299 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BC2

This is version 1.1 of the entry. See complete history

Literature

Structural and mechanistic analysis of Ca 2+ -dependent regulation of transglutaminase 2 activity using a Ca 2+ -bound intermediate state.

Sewa, A.S.Besser, H.A.Mathews, I.I.Khosla, C.

(2024) Proc Natl Acad Sci U S A 121: e2407066121-e2407066121

  • DOI: https://doi.org/10.1073/pnas.2407066121
  • Primary Citation Related Structures: 
    9BC2, 9BC3, 9BC4

  • PubMed Abstract: 

    Mammalian transglutaminases, a family of Ca 2+ -dependent proteins, are implicated in a variety of diseases. For example, celiac disease (CeD) is an autoimmune disorder whose pathogenesis requires transglutaminase 2 (TG2) to deamidate select glutamine residues in diet-derived gluten peptides. Deamidation involves the formation of transient γ-glutamyl thioester intermediates. Recent studies have revealed that in addition to the deamidated gluten peptides themselves, their corresponding thioester intermediates are also pathogenically relevant. A mechanistic understanding of this relevance is hindered by the absence of any structure of Ca 2+ -bound TG2. We report the X-ray crystallographic structure of human TG2 bound to an inhibitory gluten peptidomimetic and two Ca 2+ ions in sites previously designated as S1 and S3. Together with additional structure-guided experiments, this structure provides a mechanistic explanation for how S1 regulates formation of an inhibitory disulfide bond in TG2, while also establishing that S3 is essential for γ-glutamyl thioester formation. Furthermore, our crystallographic findings and associated analyses have revealed that i) two interacting residues, H305 and E363, play a critical role in resolving the thioester intermediate into an isopeptide bond (transamidation) but not in thioester hydrolysis (deamidation); and ii) residues N333 and K176 stabilize preferred TG2 substrates and inhibitors via hydrogen bonding to nonreactive backbone atoms. Overall, the intermediate-state conformer of TG2 reported here represents a superior model to previously characterized conformers for both transition states of the TG2-catalyzed reaction.


  • Organizational Affiliation
    • Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305.

Macromolecule Content 

  • Total Structure Weight: 78.51 kDa 
  • Atom Count: 5,235 
  • Modeled Residue Count: 657 
  • Deposited Residue Count: 694 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein-glutamine gamma-glutamyltransferase 2687Homo sapiensMutation(s): 0 
Gene Names: TGM2
EC: 2.3.2.13 (PDB Primary Data), 3.4 (PDB Primary Data), 3.5.1.44 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P21980 (Homo sapiens)
Explore P21980 
Go to UniProtKB:  P21980
PHAROS:  P21980
GTEx:  ENSG00000198959 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21980
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HB-225 (gluten peptidomimetic TG2 inhibitor)B [auth E]7synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.299 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.247 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.609α = 90
b = 71.609β = 90
c = 309.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-17
    Changes: Database references